{"doi":"10.1128/mra.01192-19","title":"Draft Genome Sequences of Strains TAV3 and TAV4 ( <i>Verrucomicrobia</i> : <i>Opitutaceae</i> ), Isolated from a Wood-Feeding Termite, and <i>In Silico</i> Analysis of Their Polysaccharide-Degrading Enzymes","abstract":"Here, we report the high-quality draft genome sequences of Opitutaceae sp. strains TAV3 and TAV4, which were isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes . Using a combination of Illumina and PacBio sequencing, we constructed nearly complete assemblies totaling 5.84 and 5.91 Mbp in length for strains TAV3 and TAV4, respectively. In addition, we report an in silico analysis of potential lignocellulose-digesting enzymes present in these strains.","journal":"Microbiology Resource Announcements","year":2020,"id":110318,"datarank":0.37470858854055655,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.08282206618225951,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.08282206618225951,"corpus_percentile":52.030633557669994,"corpus_rank":6202,"citation_count":6,"citer_count":3,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9051,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":525262,"name":"Jonathan Y. Lin","orcid":"0000-0003-4977-2506","position":1,"is_corresponding":false},{"id":525263,"name":"Jantiya Isanapong","orcid":"0000-0002-1291-2125","position":2,"is_corresponding":false},{"id":525264,"name":"Jorge L. Mazza Rodrigues","orcid":"0000-0002-6446-6462","position":3,"is_corresponding":false},{"id":526264,"name":"Malini Kotak","orcid":null,"position":0,"is_corresponding":true}],"reference_count":10,"raw_metadata":null,"created_at":"2026-07-18T23:12:57.988348Z","pmid":"31919165","pmcid":"PMC6952651","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":83.3333,"fair_a":62.5,"fair_i":20.0,"fair_r":16.6667,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 .","grounded":true,"rationale":"The paper provides GenBank accession numbers, which are persistent identifiers in the NCBI scheme. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 .","grounded":true,"rationale":"The data are deposited in GenBank (DDBJ/ENA/GenBank), a recognized data repository. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","grounded":true,"rationale":"The data availability statement points to repository records with accession numbers, corresponding to Colavizza category 3. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The final assembly for strain TAV3 has a total length of 5,844,025 bp containing 4,976 genes predicted from 32 contigs, with an N 50 value of 294,410 bp. Similarly, the TAV4 genome assembly contains 5,914,438 bp with 5,039 genes from 33 contigs, with an N 50 value of 480,638 bp.","grounded":true,"rationale":"The dataset description is given in running prose, not as an itemized inventory (section, table, or list). [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","grounded":true,"rationale":"The dataset identifiers appear only in the body text (Data Availability section), not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","grounded":true,"rationale":"The data are deposited in public repositories with no stated precondition for access. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","grounded":true,"rationale":"The paper describes the data deposition in public repositories but does not explicitly label the access level (e.g., 'open access') for the data. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","grounded":true,"rationale":"The data are not sensitive (bacterial genome sequences) and no gatekeeper is named.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No statement about when the data are available or how long they persist is provided. [majority verdict 'no' (3/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released data (e.g., FASTA, FASTQ).","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"A comprehensive in silico analysis of the carbohydrate-active enzyme (CAZy) profiles identified 433 (8.7% of total) and 431 (8.5% of total) genes in strains TAV3 and TAV4, respectively, as belonging to one of the CAZy families.","grounded":false,"rationale":"The paper uses CAZy families, a community standard vocabulary for carbohydrate-active enzymes. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier (accession, DOI, etc.) for an external resource is provided in the text.","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":16.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license is stated for the data; the CC-BY license applies to the article only.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Reads were quality checked using FastQC ( 5 ), and a hybrid assembly was performed using reads from the Illumina and PacBio runs with Unicycler v0.4.6.0.","grounded":false,"rationale":"The paper names specific software and sequencing platforms used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (e.g., README, data dictionary) is named as accompanying the data.","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is given for the data snapshot.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No custom code is mentioned; only third-party tools are used.","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"supported by NIH shared instrumentation grant 1S10OD010786-01.","grounded":true,"rationale":"An NIH grant number is provided. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No license is stated for the data; the CC-BY license applies to the article only.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named for the released data (e.g., FASTA, FASTQ).","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No custom code is mentioned; only third-party tools are used.","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","why":"The dataset identifiers appear only in the body text (Data Availability section), not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is given for the data snapshot.","gain":4.17,"priority":"useful","scored":true},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The final assembly for strain TAV3 has a total length of 5,844,025 bp containing 4,976 genes predicted from 32 contigs, with an N 50 value of 294,410 bp. Similarly, the TAV4 genome assembly contains 5,914,438 bp with 5,039 genes from 33 contigs, with an N 50 value of 480,638 bp.","why":"The dataset description is given in running prose, not as an itemized inventory (section, table, or list). [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","why":"The paper describes the data deposition in public repositories but does not explicitly label the access level (e.g., 'open access') for the data. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"A comprehensive in silico analysis of the carbohydrate-active enzyme (CAZy) profiles identified 433 (8.7% of total) and 431 (8.5% of total) genes in strains TAV3 and TAV4, respectively, as belonging to one of the CAZy families.","why":"The paper uses CAZy families, a community standard vocabulary for carbohydrate-active enzymes. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Reads were quality checked using FastQC ( 5 ), and a hybrid assembly was performed using reads from the Illumina and PacBio runs with Unicycler v0.4.6.0.","why":"The paper names specific software and sequencing platforms used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No documentation object (e.g., README, data dictionary) is named as accompanying the data.","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The whole-genome sequences and annotations for strains TAV3 and TAV4 have been deposited under the DDBJ/ENA/GenBank accession numbers NZ_LXWT00000000 and NZ_LXWU00000000 . The NCBI BioProject and BioSample accession numbers for the TAV3 project are PRJNA321366 and SAMN04992812 , respectively. The TAV3 raw reads were deposited in the SRA under accession numbers SRR10174322 (PacBio) and SRR3537542 (Illumina). The NCBI BioProject and BioSample accession numbers for the TAV4 project are PRJNA321367 and SAMN04992813 , respectively. The TAV4 raw reads were deposited in the SRA under accession numbers SRR10176387 (PacBio) and SRR3537605 (Illumina).","why":"The data are not sensitive (bacterial genome sequences) and no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier (accession, DOI, etc.) for an external resource is provided in the text.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No statement about when the data are available or how long they persist is provided. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:49:05.901057Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}